Question about guitar notes/strings?

I'm really confused because when you hold the guitar the 6th string is the one at the top isn't it? But then on tabs or whatever they are called the line representing this string is at the bottom - is that correct? Also, I'm confused, say I used the Eddie Ate Dynamite thing.. On the guitar tab this is upside down, so does that mean that the 5th string for example is the A string? (the 5th string which is really the second string if you're looking down at the guitar) Help??